[gmx-users] treating trajectory for diffusion calculations

[Dave M]

Hi All,

I have a coarse-grained simulation box with water and oil phases. Just
playing with the diffusion 'only on a single particle' (single martini
coarse bead) gave me different results when I use -rmcomm on trajectories
with and without -pbc nojump.

NOTE: selected only single bead

Same diffusion results:
gmx msd  -s md.tpr -n index.ndx -f md.xtc  # D=2.8914 x1e-5 cm^2/s
gmx msd  -s md.tpr -n index.ndx -f nojump.xtc # D=2.8914 x1e-5 cm^2/s

Different diffusion results:
gmx msd  -s md.tpr -n index.ndx -f md.xtc -rmcomm #D= 2.491e-15 x 1e-5
cm^2/s
gmx msd  -s md.tpr -n index.ndx -f nojump.xtc -rmcomm #D = 7.03e-16 x1e-5
cm^2/s

Also, I note that -rmcomm D values are very different (factor slow by e-15)
from when I don't use rmcomm. What is the correct way to treat trajectory
here before calculating msd? I have run my simulation as comm-grps whole
system (default option). I am not sure when should I use -rmcomm option (in
gmx msd) though the MSD numbers look more relevant if I don't use this.

Thanks
Dave